Namco doesn't own the right to Link but he was still in Soul Calibur II.
EA doesn't own the right to Mario, Luigi, or the Princess, however they are still in SSX on Tour and NBA Street 2.
Nintendo let them use the characters in hopes of attracting more people to the GameCube version of those...
I think it should get knocked for not having a strong multiplayer mode. Quake isn't a story based game. It is based on its multiplayer mode. I know people that are getting it solely for that aspect and will never touch the single player side.